Installation of additional softwares

We give some simple outlines to install additional softwares required by ncPRO-seq, for more information, please refer to the main site of each software:

The http://bowtie-bio.sourceforge.net/manual.shtml Bowtie Aligner (v2.0) [9].
- The latest Bowtie program can be found http://sourceforge.net/projects/bowtie-bio/files/bowtie/0.12.7 here. Users can choose the pre-compiled version for your operating system, or build your own Bowtie from the source (bowtie-*-src.zip). Users need to unzip the downloaded file. If starting with the source, users should use make command at the shell prompt to compile the program. In both ways, users should either add the directory where Bowtie binaries are located to your PATH variable, or copy/move Bowtie binaries to a directory (e.g. /usr/local/bin) in your PATH variable.
  
  The indexes of the chosen genome reference need to be prepared beforehand and set in the environment variable BOWTIE_INDEXES
The http://www.r-project.org/ R (v2.12.0) [13] and http://www.bioconductor.org/ BioConductor [6] softwares.
- There are several ways to install R program detailed in http://cran.r-project.org/doc/manuals/R-admin.html# R-project site. Here, we just show how to build R from the source. Users can choose a http://cran.r-project.org/mirrors.html site mirror close to you to download the latest R source code (R-*.tar.gz) for all platforms. You need to unpack the file and go to the unpacked directory at the shell prompt. Then for Linux/UNIX, use
```
> ./configure
> make
> su
> make install
```
  For Mac OS X, use
```
> ./configure --with-blas='-framework vecLib' 
--with-lapack --with-aqua --enable-R-framework
> make
> su
> make install
```
- To install Bioconductor, make sure that your computer is connecting to internet and use the following commands in an R command window (type R in your shell prompt, and press enter $\hookleftarrow$ ):
```
> source("http://bioconductor.org/biocLite.R")
> biocLite()
```
The R packages: http://www.bioconductor.org/packages/2.2/bioc/html/seqLogo.html seqLogo [2], http://www.bioconductor.org/packages/2.6/bioc/html/girafe.html girafe [16] and http://cran.r-project.org/web/packages/RColorBrewer/index.html RColorBrewer [11].
- To install the seqLogo and girafe package in R, use the following commands in an R command window:
```
> source("http://bioconductor.org/biocLite.R")
> biocLite("girafe")
> biocLite("seqLogo")
```
- To install the RColorBrewer package in R, use the following command in an R command window:
```
> install.packages("RColorBrewer")
```
The http://code.google.com/p/bedtools/ BEDTools suite (v2.15.0) [12] and the http://xfer.curie.fr/get/nil/2Rpz9IfJKcZ/BEDTools_MapCount_ColorTag.tar.gz bamMapCount program.
- The latest BEDTools can be downloaded http://code.google.com/p/bedtools/downloads/list here (BEDTools.*.tar.gz). Use the following commands to compile BEDTools, and copy/move all binaries in bin subdirectory to a directory (e.g. /usr/local/bin) in your PATH variable
```
> tar -zxvf BEDTools.<version>.tar.gz 
> cd BEDTools<version>
> make clean
> make all
> su
> cp bin/* /usr/local/bin
```
- The bamMapCount program is friendly shared by Assaf Gordon, which can be found http://xfer.curie.fr/get/2Rpz9IfJKcZ/BEDTools_MapCount_ColorTag.tar.gz here (BEDTools_MapCount_ColorTag.tar.gz). He integrated his programs to BEDTools. Users can unpack the whole package and compile it, then just copy/move the bamMapCount program in bin subdirectory to a directory (e.g. /usr/local/bin) in your PATH variable if you have already installed BEDTools.
```
> tar -zxvf BEDTools_MapCount_ColorTag.tar.gz
> cd BEDTools_MapCount_ColorTag
> make all
> su
> cp bin/bamMapCount /usr/local/bin
```
The http://samtools.sourceforge.net/ SAMTools suite [10].
- Users can download the latest version of SAMtools http://sourceforge.net/projects/samtools/files/latest/download?source=files here (samtools-*.tar.bz2). Make sure that you have http://www.zlib.net zlib library (v1.2.3) installed in your system before compiling SAMtools. Then use the following commands to compile the SAMtools packages, and copy/move 'samtools', `bcftools/bcftools' and other executables/scripts in `misc' to a directory (e.g. /usr/local/bin) in your PATH variable:
```
> tar -xvjpf samtools-<version>.tar.bz2
> cd samtools-<version>
> make
> su
> cp samtools /usr/local/bin
> cp bcftools/bcftools /usr/local/bin
```
The http://www.imagemagick.org/script/index.php Convert/ImageMagick utilies.
- The Convert/ImageMagick normally comes with most of modern linux/UNIX systems, but if you also want to install another version, there are a few easy steps to do which are detailed http://www.imagemagick.org/script/install-source.php#unix here. For Mac OS X, users can use http://www.macports.org/ MacPorts command as shown below to build ImageMagick in your system.
```
> su
> port install ImageMagick
```
A local server with php.
- We recommend users to install http://www.apachefriends.org/en/xampp.html XAMPP, a free and open packages consisting Apache, MySQL, and Perl/PHP/Python. To install XAMPP, you just need to download the right software version for your system and extract it. For linux/UNIX, download XAMPP and follow steps in this http://www.apachefriends.org/en/xampp-linux.html page. For Mac OS X, check this http://www.apachefriends.org/en/xampp-macosx.html page

Chongjian Chen 2012-01-26